Advantage of the JSEQ/CSSG® tool in high-resolution cell population discovery


Supplement 1.1

Brain complexity

!!!Warning!!! - below we presented data in two types interactive and static. Related to a huge amount of data in some examples [e.g., cerebellum], the interactive version can not work properly on some PCs. Recommended browser Opera


Cerebellum - mouse data



Data:

Normalized expression table
Astrocytes Aqp4 Gpc5 - Apoe Astrocytes Aqp4 Gpc5 - Tprkb Astrocytes Slc1a3 Slc7a11 - Cped1 Astrocytes Slc1a3 Slc7a11 - Ranbp3l Bergmann Gdf10 Gria1 - Gria1
Xkr4 0.2160268 0.2216736 0.2404465 0.4221899 0.7699403
Gm1992 0.0210700 0.0077600 0.0735336 0.0498822 0.1123058
Gm37381 0.0166807 0.0128804 0.0215986 0.0082632 0.0170091
Rp1 0.0498806 0.0614188 0.0074269 0.0249311 0.0491225
Sox17 0.0048606 0.0053718 0.0000000 0.0000000 0.0061107
Cell composition
Subclasses [59] Interactive  Static
Subtypes [141] Interactive  Static


Motor cortex - mouse data



Data:

Normalized expression table
Astrocytes Slc1a3 Apoe - Slc1a2 Astrocytes Slc1a3 Grin2c - Slc1a2 Astrocytes Slc1a3 Ptgds - Ptgds Endothelial Cldn5 Flt1 - Bsg GABAergic Npy Adarb2 - Grip1
Xkr4 2.717575 0.8348435 1.8546009 1.580576 6.8728476
Gm1992 0.000000 0.0191590 0.1427593 0.000000 0.2583325
Gm37381 0.000000 0.0237413 0.0000000 0.000000 0.0463138
Rp1 0.000000 0.0432075 0.0000000 0.000000 0.0453302
Sox17 0.000000 0.0000000 0.0000000 1.013113 0.0000000
Cell composition
Subclasses [18] Interactive  Static
Subtypes [30] Interactive  Static


Auditory cortex - mouse data



Data:

Normalized expression table
Astrocytes Slc1a3 Hepacam - Apoe Astrocytes Slc1a3 Hepacam - Cst3 Astrocytes Slc1a3 Hepacam - Slc1a3 Astrocytes Slc1a3 Mertk - Gpc5 Astrocytes Slc1a3 Plpp3 - Apoe
Xkr4 3.4593642 3.1257874 3.006409 1.2922381 0.8926728
Gm1992 1.4871213 1.4236178 1.233734 0.0549860 0.1668951
Gm37381 0.0325659 0.0157422 0.000000 0.0000000 0.0000000
Rp1 0.0381125 0.0136421 0.000000 0.0131356 0.0000000
Sox17 0.0000000 0.0151990 0.000000 0.0000000 0.0000000
Cell composition
Subclasses [28] Interactive  Static
Subtypes [52] Interactive  Static


Orbitofrontal cortex - mouse data



Data:

Normalized expression table
Astrocytes Slc1a3 Car2 - Cd81 Astrocytes Slc1a3 Car2 - Glul Astrocytes Slc1a3 Gpc5 - Gpc5 Astrocytes Slc1a3 Gpc5 - Slc1a3 Dopaminergic Rxfp1 Ntng2 - Ntng2
Xkr4 4.4754240 5.0894768 0.8558702 0.7277140 6.0490904
Gm1992 2.3226102 2.1724244 0.0320016 0.0000000 0.5854197
Gm37381 0.0385550 0.0517933 0.0082961 0.0000000 0.0000000
Rp1 0.0775233 0.0000000 0.0081012 0.0000000 0.0000000
Sox17 0.0000000 0.0550306 0.0081034 0.0855263 0.0000000
Cell composition
Subclasses [25] Interactive  Static
Subtypes [39] Interactive  Static


Entorhinal cortex - mouse data



Data:

Normalized expression table
Astrocytes Aqp4 Apoe - Apoe Astrocytes Slc1a3 Brinp3 - Cdh18 Astrocytes Slc1a3 Brinp3 - Gpc5 Astrocytes Slc1a3 Brinp3 - Hs3st4 Astrocytes Slc1a3 Erbb4 - Cntnap2
Xkr4 0.8525836 5.4301929 4.8089745 5.3186612 6.0951426
Gm1992 0.3703344 3.0330123 2.2403751 2.1420419 3.5548043
Gm37381 0.0071477 0.0000000 0.0000000 0.0442252 0.0192348
Rp1 0.0101238 0.0667335 0.0538529 0.0000000 0.1012159
Sox17 0.0165821 0.0329424 0.0000000 0.0463407 0.0000000
Cell composition
Subclasses [33] Interactive  Static
Subtypes [69] Interactive  Static


Hippocampus - mouse data



Data:

Normalized expression table
Astrocytes Slc1a3 Plpp3 - Apoe Astrocytes Slc1a3 Plpp3 - Cst3 Dopaminergic Cck Hs3st4 - Ptprd Dopaminergic Rxfp1 4933413l06rik - Pex5l GABAergic Npy Erbb4 - Erbb4
Xkr4 1.0848248 1.1714033 2.7680306 3.9451423 5.2902240
Gm1992 0.4413108 0.5016723 0.9104245 1.2229372 1.9764989
Gm37381 0.0000000 0.0711501 0.0000000 0.0897211 0.0000000
Rp1 0.1165463 0.0752031 0.0683943 0.0000000 0.1730269
Sox17 0.2134944 0.2914689 0.0000000 0.0000000 0.0000000
Cell composition
Subclasses [12] Interactive  Static
Subtypes [23] Interactive  Static


Striatum - mouse data



Data:

Normalized expression table
Astrocytes Slc1a3 Aqp4 - Clu Astrocytes Slc1a3 Aqp4 - Slc1a2 Cholinergic Calb1 Slc5a7 - Acly Cholinergic Tacr1 Npy - Tacr1 Endothelial Cldn5 Ly6c1 - Sparc
Xkr4 0.0000000 0.0000000 0.0000000 0.000000 0.0421118
Sox17 0.0000000 0.0000000 0.0000000 1.761456 1.9647710
Mrpl15 0.0000000 0.9133879 0.7388574 3.035198 0.5635974
Lypla1 0.9655279 0.7947375 0.0000000 4.204058 1.1343567
Tcea1 1.2686132 1.9388918 0.7489950 4.482223 1.5668944
Cell composition
Subclasses [12] Interactive  Static
Subtypes [32] Interactive  Static


Thalamus - mouse data



Data:

Normalized expression table
Dopaminergic Adcyap1 Uncx - Ndn Dopaminergic Adcyap1 Uncx - Pitx2 Dopaminergic Lmx1a Uncx - Dmrta2 Endothelial Cldn5 Igfbp7 - Sparc GABAergic Npy Asic4 - Gata3
Xkr4 0.0000000 0.0000000 0.000000 0.000000 0.0973496
Sox17 0.0000000 0.0000000 0.000000 1.989048 0.0000000
Mrpl15 1.3528010 1.5724406 2.255019 2.333679 1.7855451
Lypla1 0.9502086 0.2416054 0.435312 2.630886 1.0604708
Gm37988 0.0000000 0.0000000 0.000000 0.000000 0.0000000
Cell composition
Subclasses [12] Interactive  Static
Subtypes [32] Interactive  Static


Hypothalamus - mouse data



Data:

Normalized expression table
Astrocytes Slc1a3 Gja1 - Atp1b2 Astrocytes Slc1a3 Gja1 - Slc1a3 Astrocytes Slc1a3 Gja1 - Slc6a11 Endothelial Cldn5 Flt1 - Cldn5 Endothelial Cldn5 Flt1 - Itm2a
Xkr4 0.1478369 0.0000000 0.0000000 0.0389687 0.0426850
Gm1992 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Rp1 0.0000000 0.0000000 0.0000000 0.0786196 0.0923171
Sox17 0.0000000 0.0217464 0.0000000 3.4246754 2.6691677
Mrpl15 0.4358399 0.5520658 0.4324584 0.6034894 0.8981087
Cell composition
Subclasses [18] Interactive  Static
Subtypes [45] Interactive  Static


Brain organoids - human data



Data:

Normalized expression table
Astrocytes AGT CCL2 - AGT Astrocytes AQP4 HEPN1 - AQP4 GABAergic TAC3 DLX6-AS1 - SOX4 Glutamatergic SSTR2 RP11-93H24.3 - TUBA4A NPCs FOXG1 C4ORF32 - C11ORF96
RP11-34P13.3 0.0000000 0.000000 0.0000000 0.000000 0.0000000
RP11-34P13.7 0.0000000 0.000000 0.0057023 0.000000 0.0000000
FO538757.2 2.5167939 1.393544 1.2805036 2.050920 2.1861439
AP006222.2 2.7259739 1.445707 0.5640264 1.171028 0.8439073
RP4-669L17.10 0.0286725 0.000000 0.0053284 0.000000 0.0000000
Cell composition
Subclasses [22] Interactive  Static
Subtypes [157] Interactive  Static



Supplement 1.2

Cell subtypes function enrichment


Subtypes enrichment table
Cell_name Function_gene biological_process cellular_component molecular_function
Astrocytes Slc1a3 Hepacam - Apoe APOE cholesterol metabolic process extracellular space amyloid-beta binding
Astrocytes Slc1a3 Hepacam - Cst3 CST3 defense response extracellular space amyloid-beta binding
Astrocytes Slc1a3 Hepacam - Slc1a3 SLC1A3 L-amino acid transport plasma membrane organic acid:sodium symporter activity
Astrocytes Slc1a3 Mertk - Gpc5 GPC5 protein localization to membrane cell surface protein binding
Astrocytes Slc1a3 Plpp3 - Apoe APOE cholesterol metabolic process extracellular space amyloid-beta binding


Enrichment_tool GEDSpy



Supplement 1.3

Supplement 1.3.1


The relative expression range for each gene in every region was estimated separately




Supplement 1.3.2


AD-gene deregulation table
cell_names p_Apoe subclass_DE_Apoe global_DE_Apoe region
GABAergic Sst Nxph1 - Grip1 -> GABAergic Sst Nxph1 - Kcnmb2 0.8399968 -0.0543533 -0.0055550 auditory_cortex
GABAergic Sst Nxph1 - Kcnmb2 -> GABAergic Sst Nxph1 - Grip1 0.8399968 0.0543533 0.0487983 auditory_cortex
GABAergic Vip Adarb2 - Adarb2 -> GABAergic Npy Adarb2 - Erbb4 0.0518980 0.3750681 0.1325001 auditory_cortex
GABAergic Npy Adarb2 - Erbb4 -> GABAergic Vip Adarb2 - Adarb2 0.0518980 -0.3750681 -0.2425680 auditory_cortex
Glutamatergic Cck Tox - Pex5l -> Glutamatergic Cck Tox - Malat1 0.0000000 -1.1674819 -0.8746888 auditory_cortex
p - p-value of Wilcoxon-Test between local subtypes within an initial cluster, subclass DE - real difference between subtype and local subtypes within an initial cluster, global DE - real difference between subtype and all global subtypes separately for every region/structure


Disclaimer

The analysis was performed through the non-profit and open-source pipeline JSEQ®. Pipeline belongs to the part of the JBioSystem project in which we create complex software for bioinformatics analysis. Remember in silico analysis can not be taken for granted and must be validated in vitro or in vivo. For more information go to GitHub or contact us. The JSEQ® was created in the Department of Molecular Neurobiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences

Graphical source

Brain structures:

Human brain organoids: